The most obvious is clearly the lack of any form of live tiles/desktop/widgets. There's a few apps that I would love to get more information straight on the desktop than just a badge with a count of "actions" on it. The calendar, for example - at leas it actually shows today's date - but being able to show the next meeting at a glance would be great. Or being able to show a live stock ticker etc.
The other biggie for me is default apps. It's great that we now have Chrome on there, but I'd love to be able to get any browser link to launch that rather than Safari.
The skeurmorphic v flat thing is really just window-dressing though. Sure, there's a bit of reskinning that could be done in some of the apps, but if that's one of the biggest problems that people have with a UI that's 6 year old, then it's doing something right.